[gmx-users] Graphene topology file

Justin Lemkul jalemkul at vt.edu
Tue Jul 8 13:42:47 CEST 2014

On 7/8/14, 1:23 AM, #SUKRITI GUPTA# wrote:
> Hi Justin,
> Thanks a lot for your replies. I want to simulate a half cell with graphene
> electrode only on one side, hence i am using pbc in only xy direction i.e.
> direction of graphene sheet, so that I have a infinite size graphene sheet
> with no side effects. But if I use 3D pbc then graphene sheet effect will be
> there on the other side of the box also, which I don't want.
> Also if I use 3D PBC or 2D PBC, the major problem is that even after freezing
> graphene sheet, after doing energy minimization, the sheet remains linear but
> becomes distorted and new bonds are formed between terminal carbons. I don't
> know what is the problem with my system.

That sounds like a topology problem.  Using "periodic_molecules = yes" should 
allow for bonding across periodic boundaries, so bonds shouldn't be recognized 
between atoms at the "ends" of your sheet within the unit cell.  Is that what 
you're describing?  Images would help.  Check the topology carefully to make 
sure it has been constructed properly.  A correctly sized box with g_x2top -pbc 
should create a sensible topology.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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